I am simulating Brownian motion and its interaction with fellow molecules. Due to the large amount of combination, I am getting the error "// Codes below cannot run due to runjava:293: code too large" in public void run(). I have tried increasing the memory size of the compiler, but that doesn't help.

"increasing the memory size of the compiler"???I do not know why it could help to solve the problem?Are you allocate memory dynamically in your code? Or call the same function itself and end up in an infinite loop? Or ... There are many possibility ...